[EMBOSS] seqret/entret problems using acc from ensembl-embl
david.guzman at uniklinik-freiburg.de
Mon Nov 20 14:31:43 UTC 2006
I am experiencing a very strange problem using seqret and entret. I have
downloaded and indexed with dbiflat the database files from the Homo
sapiens subsection of Ensembl (latest version as of Nov 15th).
When I try to get one sequence with seqret or the complete entry with
entret using the AC code I got the following error message:
claudia at pc-31-18-86-200:~> seqret
Reads and writes (returns) sequences
Error: Unable to read sequence
Died: seqret terminated: Bad value for '-sequence' and no prompt
I think that the format used by Ensembl for assigning IDs and ACCs is
causing the problems. For example the first entry from the flat file:
claudia at pc-31-18-86-200:~> head
ID 1 standard; DNA; HTG; 970768 BP.
DE Homo sapiens chromosome 1 NCBI36 partial sequence 1000001..1970768
DE annotated by Ensembl
I tried replacing the ":" character of the AC line with a "_" using sed
but after indexing and I get the same error message with seqret or
entret. Is there any length limit for IDs or ACCs in EMBOSS? Is there
any workaround for this problem?
# Name Type ID Qry All Comment
# ============ ==== == === === =======
embldnahs N OK OK OK Ensembl EMBL DNA H.sapiens
DB embldnahs [
comment: "Ensembl EMBL DNA H.sapiens"]
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